The two that come to mind immediately are both from the Bad Laser Dept. -- the rosary beads in "The Road Not Taken", and the "optical pump" in "Legend of the Holy Rose".
The "Holy Rose" was certainly one of the stupidest, ugliest and most implausible props ever seen on TV (although the Black Corsage necklace is down there, too). And it's a pretty lame episode, and I want to strangle Zoe. But I love the scene where Mac gets wildly geeky when he figures out what the setup with the artifacts is supposed to do. The sheer charm of that one scene scores big for me.
So on consideration, I'm rewarding the lead statuette to the rosary beads. It's a much better episode -- Mac and Pete together are always great! -- but it's a lame MacGyverism and a weak scene.
Another Dishonourable Mention should go to the waterjet escape in "The Stringer". Should go -- but doesn't. It's cheesy, it's corny, it's implausible, and it looks unrealistic as hell on film -- but it was the last episode . . . and for the last great MacGyverism of the entire series, they found a way to make Mac fly. And I love it.